Table 2.
Differential expression of cytochrome P450 (CYP450) genes via RNA-Seq analysis of glyphosate-resistant (GR) and -sensitive (GS) C. bonariensis biotypes in response to glyphosate treatment up to 288 h after treatment. The transcriptional fold change data for the GR and GS biotypes are each expressed as the ratio of the ABC transporter gene expression from glyphosate treated to untreated individuals. Therefore, a value of 1 means the gene was neither induced nor repressed. The rightmost column represents the ratio of ratios; i.e., the magnitude of effect of being glyphosate-resistant.
| No | Contig ID | UniProt ID | Functional Annotation | Putative Localization | Transcription Fold Change | Ratio GR/GS | |
|---|---|---|---|---|---|---|---|
| GR | GS | ||||||
| CYP450_1 | DN41388_c1_g1 | O49858 | CYP450 82A3 | Membrane | 4.5 | 0.4 | 11.5 |
| CYP450_2 | DN27559_c0_g1 | Q9STK7 | CYP450 71A26 | Integral component of membrane | 3.3 | 1.0 | 3.3 |
| CYP450_3 | DN22805_c0_g1 | A0A103YCT3 | CYP450 | Uncharacterized | 4.2 | 0.7 | 6.0 |
| CYP450_4 | DN35527_c1_g1 | A0A103XYM0 | CYP450 78A5 | Integral component of membrane | 10.8 | 0.4 | 27 |
| CYP450_5 | DN15853_c0_g1 | A0A251TZE7 | CYP450 71B7 | Endoplasmic reticulum | 5.6 | 1.0 | 5.6 |
| CYP450_6 | DN34846_c0_g1 | Q9LMX7 | CYP450 78A5 | Endoplasmic reticulum | 3.5 | 0.8 | 4.5 |
| CYP450_7 | DN35866_c0_g1 | A0A251SVC5 | CYP450 76C2 | Uncharacterized | 4.0 | 0.8 | 5.0 |
| CYP450_8 | DN25141_c0_g1 | O81973 | CYP450 93A3 | Integral component of membrane | 7.3 | 3.0 | 2.4 |
| CYP450_9 | DN31873_c0_g1 | A0A103YMI2 | CYP450 94A1 | Integral component of membrane | 5.5 | 1.9 | 2.9 |
| CYP450_10 | DN73328_c0_g1 | A0A251RP29 | CYP450 82A4 | Integral component of membrane | 3.8 | 1.4 | 2.7 |
Differentially expressed genes were selected using a p-value and FDR threshold set at ≤0.001; t0 = without glyphosate treatment; t1 = with glyphosate treatment—RNA was obtained from plants collected at several timepoints up to 288 h after treatment and pooled; GR: glyphosate-resistant biotype; GS: glyphosate-sensitive biotype. The phylogenetic tree of these genes is presented in Figure S10.